Found correct mod for the Arduino Mega 2560 to avoid powering it from USB

USB HANDLING CIRCUITS IN THE MICROPROCESSOR REQUIRE USB VCC TO RUN

The reason my first attempt failed, simply removing the poly (resettable) fuse, is that the fuse is between the USB connector and the microchip which needs the USB VCC connected. I had to reinstall the fuse. 

BETTER CHANGE IS TO REMOVE A MOSFET THAT ROUTES POWER

The Arduino uses a power mosfet and a comparator to decide when the external power is adequate to run the board, disconnecting the USB VCC from the board. It does leave that wire connected to the USB circuitry in the chip, however. With the transistor removed, the USB power never gets to the board so it is always powered by the external (1130) power.

This means the board powers up and down with the main system, whether or not a USB cable is connected to anything else. When the board is powered up, the cable is active as a serial connection, exactly what I wanted to happen. 

In the picture below, the green circle shows the reinstalled polyfuse. The red circle is around the pads of the removed mosfet. 

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